Goal: count SNP difference between LTR and LTNR on a per gene basis

library(tidyverse)
── Attaching packages ───────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.0.0     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.6
✔ tidyr   0.8.1     ✔ stringr 1.3.1
✔ readr   1.1.1     ✔ forcats 0.3.0
── Conflicts ──────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
library(ggrepel)

get the vcf header

vcf.header <- system("zgrep '#C' ../input/LT.vcf.gz",intern = TRUE) 
vcf.header
[1] "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t38LTR\t42LTR\t42LTRR\t43LTR\t43LTRR\t49LTWR\t49LTWRR\t95LTWR\t95LTWRR\t99LTWR"
vcf.header <- vcf.header %>% 
  str_replace("#","") %>% #get rid of the pound sign
  str_split(pattern = "\t") %>% #split on the tabs
  magrittr::extract2(1)
vcf.header
 [1] "CHROM"   "POS"     "ID"      "REF"     "ALT"     "QUAL"    "FILTER"  "INFO"    "FORMAT" 
[10] "38LTR"   "42LTR"   "42LTRR"  "43LTR"   "43LTRR"  "49LTWR"  "49LTWRR" "95LTWR"  "95LTWRR"
[19] "99LTWR" 

get the data

snps <- read_tsv("../input/LT.vcf.gz", na = c("","NA","."),comment="#",col_names = vcf.header) %>%
  select(-ID, -FILTER) # these are empty columns
Parsed with column specification:
cols(
  CHROM = col_character(),
  POS = col_integer(),
  ID = col_character(),
  REF = col_character(),
  ALT = col_character(),
  QUAL = col_double(),
  FILTER = col_character(),
  INFO = col_character(),
  FORMAT = col_character(),
  `38LTR` = col_character(),
  `42LTR` = col_character(),
  `42LTRR` = col_character(),
  `43LTR` = col_character(),
  `43LTRR` = col_character(),
  `49LTWR` = col_character(),
  `49LTWRR` = col_character(),
  `95LTWR` = col_character(),
  `95LTWRR` = col_character(),
  `99LTWR` = col_character()
)

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snps

filter to keep snps where there is data from all samples

snps <- snps %>% 
  filter({select(., matches("[0-9]")) %>% complete.cases() })
snps
snps <- snps %>% 
  mutate(TOTAL_DEPTH= {str_extract(INFO, "DP=[0-9]*") %>% 
      str_remove("DP=") %>%
      as.numeric() }
  ) %>%
  filter(QUAL >=100,
         nchar(ALT)==1,
         TOTAL_DEPTH > quantile(TOTAL_DEPTH, 0.05),
         TOTAL_DEPTH < quantile(TOTAL_DEPTH, 0.95))
snps

unpack the information differnet samples:

samples <- colnames(snps) %>% str_subset("^[0-9]")
for (s in samples) {
snps <- snps %>%
  separate(!!s, into=paste(s,c("gt","tot.depth","allele.depth","ref.depth","ref.qual","alt.depth","alt.qual","gt.lik"),sep="_"),
           sep=":", convert = TRUE)
}
snps

next steps

keep snps that are fixed differences between LTRR and LTNR

Count per gene

snps.l <- snps %>% select(CHROM, POS, ends_with("_gt")) %>%
  gather(key="plant", value="gt", -CHROM, -POS) %>%
  mutate(respnse=str_extract(plant, "LT[NR]{1,2}"))
snps.l
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